Short small bowel patients suffer from malabsorption due to a strongly reduced small bowel surface. These patients usually get a high caloric high carbohydrate-low fat diet at oral or enteral feeding. At several points our studies demonstrate that the effect of this formula is doubtful. In these patients the intestinal flora has strongly been changed and even become characteristic due to abundant presence of lactobacilli (up to nearly 100%). In many patients with a high carbohydrate-low fat diet these bacteria both produce massive amounts of d-lactic acid and gaseous CO2, and they destroy the primary bile acids that are necessary for uptake of lipids. Thus, they cause (i) an increased risk of D-lactic acidosis and D-lactic acid-associated encephalopathy, (ii) flatulence, abdominal pain and non-infectious diarrhoea, and (iii) low uptake of fat and lipophilic vitamins. It is argued that by gradually converting the diet to a low carbohydrate-high fat diet growth of the characteristic lactobacilli can be strongly reduced and so also the mentioned inconveniences.